Human-rodent somatic cell hybrids are powerful reagents for human genome analysis. Gusella et al., Proc. Natl. Acad. Sci. USA 77: 2829-2833 (1980). Determination of the human DNA content of hybrids is typically done by conventional cytogenetic banding methods, isozyme analysis, or Southern blot analysis of a panel of DNA markers mapped to specific chromosomes. All of these methods are labor-intensive, and only a complete cytogenetic analysis assays for the presence or absence of whole chromosomes. However, the sensitivity of conventional cytogenetic methods is limited, and small pieces of human chromatin may go undetected or not be accurately identified as to chromosome of origin.
Recently, a method was described by Nelson et al. (Proc. Natl. Acad. Sci. USA 86: 6686-6690 (1989)) for specific amplification of human DNA in somatic cell hybrids using the polymerase chain reaction (PCR) and primers directed at the human-specific portion of Alu, a short interspersed repetitive element (SINE) present in approximately 10.sup.6 copies in mammalian genomes. Using a single Alu primer, amplification will occur whenever two Alu elements are less than 5 kilobases apart and lie in inverted orientation to each other. This strategy has been extended (Ledbetter et al., Genomics 6: 475-481 (1990)) to the second major class of interspersed repetitive sequence, the L1 element, a long interspersed repetitive sequence (LINE) present in 10.sup.4 -10.sup.5 copies per genome in mammals. Use of a primer directed at the human L1 sequence, L1Hs, produces fewer amplification products than with Alu, consistent with its lower abundance in the genome. Thus, human DNA amplification in interspecific hybrid cells can be achieved by PCR using primers directed at human-specific sequences of different classes of interspersed repetitive sequences (IRS-PCR).
Ledbetter et al. (Genomics 6: 475-481 (1990)) also demonstrated the utility of PCR amplification from primers complementary to interspersed repeated sequences for analysis of the human component of a somatic cell hybrid. By running the amplification products on a gel, it was observed that a series of chromosome specific discrete bands were produced reproducibly. This is a simple and reproducible technique which does not require labeling of the PCR amplified product.